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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV EPITOPE-SCAFFOLD 4E10_1VI7A_S0_002_N 4E10 FV COMPLEX
 
Authors :  M. A. Holmes
Date :  21 Jan 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  H,I,J,K,L,M,N,O,S,T,U,V
Biol. Unit 1:  H,K,L,O,S,V  (1x)
Biol. Unit 2:  I,J,M,N,T,U  (1x)
Keywords :  Epitope-Scaffold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. E. Correia, Y. E. Ban, M. A. Holmes, H. Xu, K. Ellingson, Z. Kraft, C. Carrico, E. Boni, D. N. Sather, C. Zenobia, K. Y. Burke, T. Bradley-Hewitt, J. F. Bruhn-Johannsen, O. Kalyuzhniy, D. Baker, R. K. Strong, L. Stamatatos, W. R. Schief
Computational Design Of Epitope-Scaffolds Allows Induction Of Antibodies Specific For A Poorly Immunogenic Hiv Vaccine Epitope.
Structure V. 18 1116 2010
PubMed-ID: 20826338  |  Reference-DOI: 10.1016/J.STR.2010.06.010

(-) Compounds

Molecule 1 - 4E10_1VI7A_S0_002_N (T88)
    Chains: S, T, V, U
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
    Other Details: THE AUTHOR STATES THAT THE EPITOPE-SCAFFOLD IS BASED ON THE RIBOSOME RECYCLING FACTOR FROM VIBRIO PARAHAEMOLYTICUS (PDB ID 1IS1).
 
Molecule 2 - FV 4E10 HEAVY CHAIN
    Chains: H, I, K, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FV 4E10 LIGHT CHAIN
    Chains: L, M, O, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : HIJKLMNOSTUV
Biological Unit 1 (1x): H  KL  OS  V
Biological Unit 2 (1x):  IJ  MN  TU 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3LH2)

(-) Sites  (0, 0)

(no "Site" information available for 3LH2)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2I:22 -I:96
3J:22 -J:96
4K:22 -K:96
5L:23 -L:89
6M:23 -M:89
7N:23 -N:89
8O:23 -O:89

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Ser M:7 -Pro M:8
3Ser O:7 -Pro O:8
4Ser N:7 -Pro N:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LH2)

(-) Exons   (0, 0)

(no "Exon" information available for 3LH2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains d3lh2h_ H: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeeeee...eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 H   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTLGKPIGAFAHWGQGTLVTVSSLEHHH 132
                                    11        21        31        41        51        61        71        81        91       101||     115       125       
                                                                                                                              102|                         
                                                                                                                               107                         


Chain I from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains d3lh2i_ I: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeeeee...eeeeeeee...eeeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 I   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSSLEHHHH 133
                                    11        21        31        41        51        61        71        81        91       101||     116       126       
                                                                                                                              102|                         
                                                                                                                               108                         


Chain J from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains d3lh2j_ J: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 J   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGAGWLGKPIGAFAHWGQGTLVTVS 126
                                    11        21        31        41        51        61        71        81        91       101       111       121     


Chain K from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d3lh2k_ K: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lh2 K   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGAGWLGKPIGAFAHWGQGTLVTVSS 127
                                    11        21        31        41        51        61        71        81        91       101       111       121      


Chain L from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d3lh2l_ L: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 L   0 AEIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKL 109
                                     9        19        29        39        49        59        69        79        89        99       109


Chain M from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d3lh2m_ M: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3lh2 M   1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVK 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain N from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d3lh2n_ N: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 N   0 AEIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKL 109
                                     9        19        29        39        49        59        69        79        89        99       109


Chain O from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d3lh2o_ O: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lh2 O   0 AEIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKL 109
                                     9        19        29        39        49        59        69        79        89        99       109


Chain S from PDB  Type:PROTEIN  Length:64
                                                                                                
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeee....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 3lh2 S   6 HLTEYTLQANWFDITGILWLLGQVDGKIINSDVQAFVLLRVALPAKVEFSAKLADFSGGSLQLL  71
                                    15        25        35        45    ||||57        67    
                                                                       50|||                
                                                                        52||                
                                                                         53|                
                                                                          55                


Chain T from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 3lh2 T   7 LTEYTLQANWFDITGILWLLGQVDGKIINSDVQAFVLLRVALPAAKVAEFSAKLADFSGGSLQLLAI  73
                                    16        26        36        46        56        66       


Chain U from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 3lh2 U   7 LTEYTLQANWFDITGILWLLGQVDGKIINSDVQAFVLLRVALPAAKVAEFSAKLADFSGGSLQLLAIE  74
                                    16        26        36        46        56        66        


Chain V from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhh......ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 3lh2 V   7 LTEYTLQANWFDITGILWLLGQVDGKIINSDVQAFVLLRVALPAAKVAEFSAKLADFSGGSLQLLAIE  74
                                    16        26        36        46        56        66
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LH2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LH2)

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  Cis Peptide Bonds
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser M:7 - Pro M:8   [ RasMol ]  
    Ser N:7 - Pro N:8   [ RasMol ]  
    Ser O:7 - Pro O:8   [ RasMol ]  
 
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  3lh2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3LH2)

(-) Related Entries Specified in the PDB File

3lef 3lf6 3lf9 3lg7 3lhp